annotate cmstat.xml @ 1:55bb96edfc07 draft

Uploaded
author bgruening
date Thu, 24 Apr 2014 15:02:05 -0400
parents 652f9d550531
children fac157e22e1b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
2 <description>for covariance model (cmstat)</description>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
3 <requirements>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
4 <requirement type="package">infernal</requirement>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
5 <requirement type="package" version="1.1">infernal</requirement>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
6 <requirement type="package" version="8.21">gnu_coreutils</requirement>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
7 </requirements>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
8 <command>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
9 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
652f9d550531 Uploaded
bgruening
parents:
diff changeset
10 ## it will be converted to a tab delimited file and piped to Galaxy
652f9d550531 Uploaded
bgruening
parents:
diff changeset
11 temp_tabular_output=\$(mktemp);
652f9d550531 Uploaded
bgruening
parents:
diff changeset
12
652f9d550531 Uploaded
bgruening
parents:
diff changeset
13 cmstat
652f9d550531 Uploaded
bgruening
parents:
diff changeset
14
652f9d550531 Uploaded
bgruening
parents:
diff changeset
15 #if str($cm_opts.cm_opts_selector) == "db":
652f9d550531 Uploaded
bgruening
parents:
diff changeset
16 $cm_opts.database.fields.path
652f9d550531 Uploaded
bgruening
parents:
diff changeset
17 #else:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
18 $cm_opts.cmfile
652f9d550531 Uploaded
bgruening
parents:
diff changeset
19 #end if
652f9d550531 Uploaded
bgruening
parents:
diff changeset
20
652f9d550531 Uploaded
bgruening
parents:
diff changeset
21 > \$temp_tabular_output
652f9d550531 Uploaded
bgruening
parents:
diff changeset
22 ;
652f9d550531 Uploaded
bgruening
parents:
diff changeset
23
652f9d550531 Uploaded
bgruening
parents:
diff changeset
24 ## 1. replace all lines starting # (comment lines)
652f9d550531 Uploaded
bgruening
parents:
diff changeset
25 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
652f9d550531 Uploaded
bgruening
parents:
diff changeset
26 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
652f9d550531 Uploaded
bgruening
parents:
diff changeset
27
652f9d550531 Uploaded
bgruening
parents:
diff changeset
28 </command>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
29 <inputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
30 <conditional name="cm_opts">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
31 <param name="cm_opts_selector" type="select" label="Subject covariance models">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
32 <option value="db" selected="True">Locally installed covariance models</option>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
33 <option value="histdb">Covariance model from your history</option>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
34 </param>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
35 <when value="db">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
36 <param name="database" type="select" label="Covariance models">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
37 <options from_file="infernal.loc">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
38 <column name="value" index="0"/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
39 <column name="name" index="1"/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
40 <column name="path" index="2"/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
41 </options>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
42 </param>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
43 </when>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
44 <when value="histdb">
652f9d550531 Uploaded
bgruening
parents:
diff changeset
45 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
46 </when>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
47 </conditional>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
48 </inputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
49 <outputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
50 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
51 </outputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
52 <help>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
53
652f9d550531 Uploaded
bgruening
parents:
diff changeset
54
652f9d550531 Uploaded
bgruening
parents:
diff changeset
55 **What it does**
652f9d550531 Uploaded
bgruening
parents:
diff changeset
56
652f9d550531 Uploaded
bgruening
parents:
diff changeset
57 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
58
652f9d550531 Uploaded
bgruening
parents:
diff changeset
59
652f9d550531 Uploaded
bgruening
parents:
diff changeset
60 Output format
652f9d550531 Uploaded
bgruening
parents:
diff changeset
61 -------------
652f9d550531 Uploaded
bgruening
parents:
diff changeset
62
652f9d550531 Uploaded
bgruening
parents:
diff changeset
63 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
652f9d550531 Uploaded
bgruening
parents:
diff changeset
64 tabular format.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
65
652f9d550531 Uploaded
bgruening
parents:
diff changeset
66 The columns are:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
67
652f9d550531 Uploaded
bgruening
parents:
diff changeset
68 (1) The index of this profile, numbering each on in the file starting from 1.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
69 (2) The name of the profile.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
70 (3) The optional accession of the profile, or ”-” if there is none.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
71 (4) The number of sequences that the profile was estimated from.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
72 (5) The effective number of sequences that the profile was estimated from, after Infernal applied an effective sequence number calculation such as the default entropy weighting.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
73 (6) The length of the model in consensus residues (match states).
652f9d550531 Uploaded
bgruening
parents:
diff changeset
74 (7) The expected maximum length of a hit to the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
75 (8) The number of basepairs in the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
76 (9) The number of bifurcations in the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
77 (10) What type of model will be used by default in cmsearch and cmscan for this profile, either ”cm” or ”hmm”. For profiles with 0 basepairs, this will be ”hmm” (unless the --nohmmonly option is used). For all other profiles, this will be ”cm”.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
78 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
652f9d550531 Uploaded
bgruening
parents:
diff changeset
79 sensus position. This is what the default entropy-weighting method for effective sequence
652f9d550531 Uploaded
bgruening
parents:
diff changeset
80 number estimation focuses on, so for default Infernal, this value will often reflect the default
652f9d550531 Uploaded
bgruening
parents:
diff changeset
81 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
82 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
652f9d550531 Uploaded
bgruening
parents:
diff changeset
83 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
84
652f9d550531 Uploaded
bgruening
parents:
diff changeset
85
652f9d550531 Uploaded
bgruening
parents:
diff changeset
86 For further questions please refere to the Infernal Userguide_.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
87
652f9d550531 Uploaded
bgruening
parents:
diff changeset
88 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
652f9d550531 Uploaded
bgruening
parents:
diff changeset
89
652f9d550531 Uploaded
bgruening
parents:
diff changeset
90
652f9d550531 Uploaded
bgruening
parents:
diff changeset
91 How do I cite Infernal?
652f9d550531 Uploaded
bgruening
parents:
diff changeset
92 -----------------------
652f9d550531 Uploaded
bgruening
parents:
diff changeset
93
652f9d550531 Uploaded
bgruening
parents:
diff changeset
94 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
652f9d550531 Uploaded
bgruening
parents:
diff changeset
95
652f9d550531 Uploaded
bgruening
parents:
diff changeset
96 **Galaxy Wrapper Author**::
652f9d550531 Uploaded
bgruening
parents:
diff changeset
97
652f9d550531 Uploaded
bgruening
parents:
diff changeset
98 * Bjoern Gruening, University of Freiburg
652f9d550531 Uploaded
bgruening
parents:
diff changeset
99
652f9d550531 Uploaded
bgruening
parents:
diff changeset
100 </help>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
101 </tool>